Intertwined Under Reconstruction
by CutePiglet
Summary: Year 2417. In order to find true love, a boy and a girl switch hearts at the age of 16. Exactly one year later, they will find out if they were meant to be together. If not, both hearts will stop beating forever. Yami Takashi doesn't know anything about this vulgarity, nor did he know that he was going to be part of the biggest experiment yet: A swap between two boys. YxYY
1. Chapter 1

**Author's note: **If you're new to this story, please skip to chapter 2 right away for an important message. Thank you!

* * *

_"We need a moment, dear. Why don't you go unwrap some of the presents we got you?" Megumi Mori stared at her mother with her unusual red colored eyes. Her straight black hair fell in front of said eyes when she lowered her head to look at the several colorful wrappings. She gave them a nod and pretended to reach out for one of the boxes while her parents went upstairs._

_Her parents had been acting strange today. It was her 15th birthday, so she had expected everything to be perfect on such a lovely day as her birthday. But the exact opposite happened: Her mother had been wearing a dreadful smile and her father had that worried frown on his face. She barely paid any attention to the new hairbrush her parents had given her and decided to find out why her parents had acted like a pair of zombies._

_Luckily, the stairs were not made of creaky wood, or any other material that would betray her. She carefully made her way upstairs and tiptoed towards her parents' room. Her entire body froze when she heard her a soft sob. She had never heard her mom cry before._

_"I don't want to l-lose her." Megumi wrapped her pale fingers around the doorframe and peeked around the corner. Her parents were sitting on their made bed, holding each other's hands. There were dried tears on her mother's beautiful face._

_"You won't."_

_"Why can't we just tell her?"_

_Her father's face dropped and he let out a soft sigh through his nose. He scooted closer to his wife, wrapped a strong arm around her shoulder and mumbled, "You and I both know that we can't do that. We will end up in jail and our daughter will have to live with strangers. It's illegal."_

_"Do you think she will die…?"_

_"Not if she finds the one."_

_The more Megumi listened to her parents, the more she wanted to scream for help. Placing one hand on her chest, she squeezed her clothes, feeling the strong muscle beating steadily. She shook her head and ran to her room, tears falling from her eyes._

* * *

**14th of April, 2417**

"Oi! Yami, get up! We'll be late for school!"

Said person almost fell out of bed at the loud voice right next to his ear. His body was tangled up in the sheets and his face met the floor in a very painful way.

"You are so dead for that," Yami mumbled against the cold floor. He heard a nervous chuckle before he felt a pair of hands under his arms to pull him up. Two brown eyes looked him up and down to check if he was okay and the owner of those eyes rubbed the back of his neck.

"Sorry, bud. But you always sleep through the alarm clock. I had to do something."

"Maybe you could shake me awake, and not yell in my ear, Jounouchi-kun." Yami walked up to the closet they shared and looked for his uniform. While he was doing that, he could hear his best friend shuffling around, getting ready for school himself. Sharing a room with your best friend did have its benefits, but getting a wake-up call everyday was definitely something that had not been on his wish list.

"Can't wait to celebrate your birthday, Yami. I think my mom is planning something because she was acting strange yesterday." Yami pulled his white shirt over his head with a small smile, feeling pumped. He had completely forgotten about the fact that he had turned sixteen today and that they were probably going to have a delicious cake when they came home from school.

"She always acts suspicious one day before our birthday because she knows we know that she's planning something," he said with a small smirk. Jounouchi nodded and chuckled a bit, pulling his jacket over his shoulders. "Your birthday is in three days, you know. And you never told me what you wanted."

Jounouchi tapped his chin thoughtfully, looking at the white ceiling with his brown eyes. Yami rolled his eyes at him before he lightly punched him in the shoulder and went to the bathroom.

"You have to give me some time to think!" a muffled voice called out to him after he had closed the door.

"You had an entire year!" Yami called back with a small laugh.

The other was silent for a while before he murmured a quiet answer, "Point taken."

When both of them were ready to go to school, they went downstairs to have some breakfast. The white walls in the living room glistened beautifully in the morning light, as if Jounouchi's mother, Ami, had just cleaned them. Said mother came walking into the living room, holding a small cupcake in her hands. Her brown eyes shone kindly behind her round glasses. Her white apron was covered in flour, patches of chocolate and some dough, obviously indicating she had been baking all morning.

"Good morning, you two. Happy birthday, Yami." She bent down to give him a small kiss on his cheek and handed him the cupcake. Yami thanked her and nibbled on the chocolate layer on top of the cupcake, smiling at the sweet taste. "Katsuya, do you still have enough money to take the bus?"

Jounouchi emptied his pockets with a slightly red face. "Eh…"

Ami shook her head with a small smile and got out a round card. "Here. This should be enough for both of you. And don't go shopping with it because I will find out." She pointed over her shoulder at a small screen above the fridge. The screen showed the family's bank account, including hers and her husband's. "All right. Have some breakfast and then leave, I don't want you to be late."

Domino Spring was already filled with many students before the last bell would ring. Every single student was standing in the hallway, chatting happily about their weekends and their plans for the upcoming birthdays. When Yami and Jounouchi walked through the doors, many people walked up to them to wish Yami a happy birthday. Even though it was nice, Yami didn't like being popular at all.

The only reason he was part of the popular gang was because Jounouchi had a thing for one of the most popular girls in school: Mai Kujaku. Jounouchi had managed to make his way to the gang and had dragged Yami along, not wanting to leave him behind.

Yami did have some friends, but he never got the chance to talk to someone else besides the popular people. Domino Spring was the biggest school in the era, besides the other three Season schools. At least 6,000 students attended this school and Yami knew about ten out of them all. He saw new people almost every day and found it weird that he knew no one, and yet, everyone knew him.

The bell rang and the hall went empty as everyone walked to their first class. Yami and Jounouchi had their first class together, so they took the elevator to the third floor. The school year was almost over and Yami could barely believe that he was now officially an adult and that he had to find a job when he got his diploma.

"Can't believe high school is almost over," he mumbled after the elevator had let out a small beep.

"Yeah. Don't forget to laugh at Domino Summer students because their school year ends three months later," Jounouchi said with a small laugh. Yami grinned at the mockery, shaking his head a bit. They walked up to the classroom and Yami took a random seat between the many students.

"All right. Today we'll discuss probabilities one more time. You all know the drill: No talking unless you get stuck, no drinking because you don't want your Downloader to break. Wear it for at least 45 minutes this time, I will deactivate them once the time's up. Put the Downloaders on."

Yami looked at his shining blue desk with a small device on it. It looked like a sparkly iron hat to him and he knew it was going to be very heavy this time. Probabilities had so many chapters, which meant he had to focus extra hard to be able to download all the information to his brain.

The teacher tapped on his desk. The Downloaders turned green and everyone put them over their heads. The device was so big that it dropped down Yami's eyes so he could not see anything. A small screen appeared in front of his eyes and a cool voice spoke into his ear.

_"Welcome to chapter 13: Probabilities. Please wait for your teacher's instructions before activating the system."_

"Everyone ready? Click on paragraph one and two. When you're finished with those paragraphs, go to the next two. We'll go to the last two paragraphs tomorrow morning. Good luck."

For some reason, the day went pretty fast because before Yami could comprehend what was going on, he was walking through the front doors of Domino Spring again. Jounouchi followed him after he had wrapped an arm around his shoulder, ranting on about that one math class they had in the morning. When they walked past the school gates, someone bumped into Yami, almost causing him to lose his balance.

"Excuse me," a low voice said gently. It was a man in a black suit and he quickly bowed before he walked away. Yami rubbed his throbbing shoulder, frowning faintly at the stranger's back.

"Wonder what his problem was," Jounouchi mumbled.

"He was probably in a hurry. Come on, let's go." They continued to walk, chatting about homework, but mainly about what they were going to do for Yami's sixteenth birthday. Jounouchi loved talking about the different cakes his mother could bake and about how he got him this one awesome present. He casually started talking about inviting Mai too, and that Yami should probably invite Mana over as well.

"I already told you that my love life is out of the question. I don't care about that," Yami said with a small shrug. It was true, he was not interested in anyone. After all, he had just turned sixteen and had never even though about being in a relationship before. Everyone tried to force Mana on him, saying that they were the "perfect couple", but he simply refused to believe it.

Mana was a good friend of his and she was pretty, but she was not really his type. They were the complete opposite of each other ("Opposites attract," Jounouchi told him) and he did not think he would be able to keep a steady relationship with someone like her.

He was so lost in his train of thoughts that he barely noticed he had stopped walking and that Jounouchi had already turned around the corner. Blinking, he started to run to catch up with him, but he was roughly grabbed around his waist.

A very strong arm was wrapped around his body and that same arm pulled him against a broad chest. He was about the yelp, but another arm wrapped a cloth around his mouth. The cloth smelled funny, like alcohol, and made him feel a bit lightheaded. His shoulders felt very light when his backpack was lifted off his body and he could hear the zipper of it.

"Yeah, that's definitely him. Found his ID. Yami Takashi, born 14th of April, 2401. No sign of any health issues, lives with the Jounouchi's, both parents are dead. Take him." Yami's eyes widened at the information. His body was thrown over someone shoulder and he struggled for all he was worth, feeling the adrenaline pumping through his veins. He looked up to see the corner he was heading towards, the corner where he would have been safe.

He tried to call for Jounouchi's name, but all that came out was a muffled yelp which earned him a slap on his lower back, right where his tailbone was, and he grunted in pain. That was a rather sensitive spot because he could feel a sharp pain shooting through his entire back and he was obligated to hold still if he didn't want to be in pain.

"Shut it, kid. You'll be fine."

That was probably the biggest lie he had ever heard in his life. He was going to be everything but fine with these guys, knowing he could never beat them on his own. He carefully looked them up and down. They were all dressed in black suits, but underneath all of that, he could still see the muscles, as if they had just gotten back from the gym.

He could feel his heartbeat in his ears. So many gruesome stories filled his head; maybe they were bringing him to some mental institute, or going to cut off his limbs, or murder him, or worse… For the first time in his life, Yami felt helpless. If only Jounouchi had waited for him, then none of this would have happened.

"Here we are." Yami could hear a door sliding open and suddenly, he was thrown onto a hard surface. Before he could even comprehend what was going on, the two guys jumped on him and bound his wrists together on his back. He tried to fight back by trying to kick them or bite them, but they simply ignored him and chuckled at his useless attempts.

"And no peeking." The cloth around his mouth (which was now covered in saliva) was removed and wrapped around his eyes this time and he let out a breathless cry as he felt something colliding with his back. "Don't get any funny ideas, you hear? Hold on tight, it's going to be a bumpy ride."

Darkness had completely taken over his vision, he did not even get a chance to take in his surroundings before they blinded him. The only thing he had seen was the glimpse of the grey inside of the vehicle they were in. The engine let out a loud roar, the van came to life, and he swayed on the spot as they started driving.

There was no way he was going to get his hands free for there were probably about ten tight knots.

The thing that had bumped into his back was still there. Yami frowned when he slightly pressed against the hard surface; he could feel a spine. His eyes widened behind the cloth and he moved his head to the right, feeling some random hairs brushing against his jawline.

"… Hello?" he tried softly. He had to make sure he was not alone in here, if there was another person there, they could come up with a plan to get themselves out of this mess. He waited anxiously, trying to get his breathing under control; it sounded wheezy and shaky. He had never been this scared in his life and he knew it was best not to panic, but that was easier said than done.

"…Hi," a shaky voice finally replied after a good twenty seconds.

"They took you as well?"

"Y-yeah." It was a boy. Not very old, but not young either because his voice was not high pitched, or anything. Probably a teenager. A thing they had in common.

"You okay?" That was a stupid question. Of course the other was not okay, he was probably just as scared as him, maybe even worse.

"… Fine, fine. 'm Fine." Yami smiled faintly at the soft voice. He squirmed a bit to try to move his fingers a bit and after a while of rather awkward fiddling, he could feel the other's cold hands. They were shaking, just like his voice and he wrapped a couple of fingers around them since he couldn't move his entire hand.

"It's going to be okay. You're going to be okay…" he said gently. He was craving for some answers, some warmth, some comfort, someone to tell him this was some crazy dream he was having… This couldn't be real. He had a normal life, lived happily with Jounouchi and his family, got average grades and had never even gotten into a fight.

He could have been home right now, relaxing on the couch with Jounouchi, maybe watch some stupid cartoons and celebrate his birthday. The fact that this was all happening on his birthday seemed to make it worse. All he wanted to do today was to spend time with Jounouchi and his parents and go out for dinner tonight.

The boy spoke up again, and this time, he sounded different. "Wait, I think I know your voice. Aren't you one of those popular kids at Domino Spring?" Yami was a bit taken aback by the steadiness of the boy's tone now. It sounded more like an accusation than a question.

"Yeah," he answered, his voice rising up a bit as if he was not entirely sure of his answer.

"And I thought popular kids had it all. Maybe they're going to ask your parents to pay 1 billion yen to set you free."

A nasty taste entered Yami's mouth and he blurted out, "My parents are dead."

That shut the other up. They fell into an uncomfortable silence, moving slightly every now and then to get into a more comfortable position. The ground below them shook gently as the van kept moving. Yami noticed he was still holding the boy's hand with his fingers, and right then, he felt the other squeezing his fingers softly, muttering a small apology under his breath.

* * *

"Mom! _Mom!_" Ami looked up from the chicken soup and turned to her son. His blond hair was a complete mess, as if he had run his hand through it at least twenty times and his face was covered in sweat. The moment Ami saw the look in her son's eyes, she knew why he was standing there.

Fully turning to him, she managed to smile. "What is it, Katsuya?"

"Yami's gone missing! One minute we were talking and suddenly he was gone! I know he wanders off sometimes, but he still hasn't come back and…" his voice shook and he looked up, his eyes filling up with angry tears. "That bastard hasn't even called me, or anything. It's been hours and he hasn't even—"

Ami hated to see her son like this. He knew Yami was his closest friend, they were even closer than brothers and she could only imagine what it was like to lose a best friend. All she could do was smile reassuringly and tell him that everything was going to be okay.

"I think he'll be back tonight. After all, it's not like him to run off, especially on his birthday." The words hurt. They hurt her because Katsuya's birthday was in a couple of days and she was dreading the fact he was going to be sixteen, too. The heart in her chest picked up the pace and was beating painfully against her ribs.

Katsuya walked up to her and gave her a look. "Do you really think so? You look pretty worried to me."

"Of course I am," she replied, still smiling. "He's like a son to me, too. But I'm sure he'll be back. Have you tried calling him?"

"He won't pick up," Katsuya said, kicking at the ground with a dull look in his eyes. He shoved his hands in his pockets and lowered his head so his brown eyes were hidden by his blond bangs. "Some friend he is." With a sigh, he walked out of the small kitchen, leaving Ami alone. She winced when Katsuya gave the wooden door a loud kick when he closed it behind him.

Her husband walked in after that, looking her up and down. His eyes held nothing but sorrow, and her eyes mirrored his.

"All we can do is wait," he said softly.

A tear trickled down her cheek and she whispered, "Please let it be a match. Please…"

* * *

"What do you mean this was the only match? I thought we agreed to use this girl." Said girl was yanked up from her seat and yelped in pain as the strange man tightened his grip around her slender arm. "They're about the same age and go to the same school."

The girl looked up at him, her green eyes silently begging him to let go of her arm. The man ignored her and gave the others a hard glare with his cold blue eyes. They were surrounded by at least ten doctors and were standing in one of the many hallways of the gigantic building.

"I know that, Kaiba. But like you said, they're _about_ the same age. We can't have that, she won't be a match then. Besides, Takashi already knows her and that's against the rules. The two patients must have no connection whatsoever, that is law."

Kaiba dropped the girl's arm and she immediately started rubbing it with her other hand. He looked at the other girl who looked equally scared and disorientated. Her blue eyes matched his perfectly, and so did their brown hair.

"What about her?"

The man in front of him shook his silver hair out of his face and pulled out a chart. "Let's see. Anzu Mazaki, born 17th of April, 2401, goes to Domino Spring and has known Yugi Mutou since kindergarten." The man looked up, his copper eyes narrowing in annoyance. "Don't think you did a good job by getting these two girls here today, Kaiba. She's simply not a match. I understand your point of view, though. The experiment has never been performed on two patients with the same gender."

"Exactly. How could they ever be a match?"

"Oh, I love the idea of experimenting. I really want to know what happens when the doctors are finished with the operation. If this works, we'll start a new era and, more importantly," he grinned at his own words. "We'll make two people happy again. And isn't that far more valuable than the fact they're both males?"

"Pegasus…" Kaiba grunted, gritting his teeth.

"Take these two girls to their rooms. And make sure they don't have any electronic devices. Don't want them ruining our plans, right?" He looked at the two girls and winked teasingly, causing the two girls to shift uncomfortably in their seats. Kaiba muttered something under his breath before he grabbed their arms and dragged them to the elevator. Another man followed him to make sure the girls could not escape and gave Pegasus a thumbs-up.

"Good. Now then," Pegasus turned around and looked at the two white doors, folding his arms over his chest. "They should be done by now."

As if on cue, the doors opened and a large hospital bed rode out of the operation room. A loud shriek filled the air and the men looked up to see one of the girls trying to escape from Kaiba's iron grip.

"Oh my god… Yugi! _Yugi_!" Her eyes swam with tears and Kaiba groaned in annoyance before he pulled her into the elevator and closed the doors. The men turned back to the two patients and followed the doctors who were bringing the two boys to their rooms. Pegasus had seen these two a few minutes before the operation and noticed the similarities right away.

These two could either be the perfect match or the complete opposite. Both patients were still unconscious, looking quite peaceful because of their closed eyes and neutral expression. Their bodies were covered by the duvets, but Pegasus could still see the bandages wrapped around their chests and the black armband clasped around their right wrist.

"How did it go?" he spoke up after he had studied them carefully. One of the doctors, the leader, looked up at him and gave him an approving nod.

"Pretty smoothly. I barely noticed anything out of the ordinary during the operation. Both seem stable now. We already checked if their pupils respond to light and if they had any internal bleedings, but everything seems fine. They should wake up in a few minutes and you can inform them then. Once we reach the room, we shall activate the armbands."

"Thank you. Ah, here we are." They reached a large white room, which looked like any other ordinary room and rolled the beds to the corners. The beds were facing each other now so that the two patients could look at each other. The blue curtains were closed, hiding the dark sky from view. The two heart monitors next to the beds beeped softly with each steady heartbeat. Two men walked up to the patients and grabbed their right wrist, exposing the two matching bracelets.

"Any minute now," the surgeon said. Everyone waited patiently for the boys to show any signs of consciousness and braced themselves in case one of them acted up.

After a few seconds, one of the two moaned softly and groggily opened his eyes. Miraculously, the other did the same and Pegasus quickly snapped,

"Now!" The two men who were holding their wrists, pressed one button on the bracelet to activate them. A timer appeared, the red digits shining brightly in the dim light room. His loud voice had woken them up because both boys looked around, confused and disorientated. "Good job, everyone. We have two conscious boys."

Some men chuckled at this and others clapped.

One of the boys looked down at himself, his eyes widening when he saw his bandaged chest. His blood red eyes looked a bit dull, but alert when he looked up at them.

"What is—"

"Calm down… Yami, was it?" The teenager looked slightly confused before he nodded half-heartedly. "We mean no harm. I shall explain everything. But first I want to make sure that you should know you should not panic, or anything. You just woke up from a very intensive surgery and we shouldn't rush into things. Try to keep calm. Can you promise me that?"

Both of them nodded slowly. Yami's eyes drifted off to the other boy, blinking.

"Yami, this is Yugi Mutou. He was born exactly sixteen years ago, just like you, and therefore, shares the same fate. Both of you were taken today to undergo a very special surgery," Pegasus stated with a small grin. "If you take a look at your right wrist, you will see a timer on that armband of yours. In exactly 364 days, 23 hours and 55 minutes you two will receive the answer you've both been waiting for your entire lives."

"Which is?" Yugi spoke up.

"If you two are meant to be together for the rest of your lives." Two pair of eyes widened at the incredulous statement. "For you see, when two people turn sixteen, we will swap their hearts. We have done this operation for many, many years and it has worked for many people. It looks like the operation was a success because you seem stable."

Pegasus smiled encouragingly at them when he finished his short explanation. Yugi was looking down at the bracelet, running his fingers over the smooth surface. There was a lock on it, right over the inside of his wrist, so he could not take it off without the needed key. Yami, on the other hand, was clutching the bandages on the left side of his chest, where a stranger's heart was beating.

"… What happens when we aren't meant to be together?"

Everyone went silent. Yugi was looking at the other patient, his lips thinning, as if he was scared to hear the answer. Pegasus sighed and held up his hands; his smile had disappeared completely.

"Your hearts will give you the answer when the timer runs out. If it was meant to be, then nothing will happen and you can live together as a happy couple," he said matter-of-factly. "If not, then both of you will die of a heart attack."


	2. Chapter 2

**Author's note: **I'm very sorry for taking advantage of posting a new chapter and making you all excited, but since you are not allowed to only write author's notes in a chapter, I made a mini-chapter and hopefully it will clear things up.

* * *

He had been following the same voice all this time. Darkness surrounded him and teasingly brushed against his skin, but there was one bit of light at the end of the tunnel and he kept wandering around, still following that voice.

"_Wake up, Yami! Please wake up!_"

Finally, Yami's eyes flew open and he sat up straight, staring into a pair of worried violet eyes. He instantly reached for his chest, but there were no bandages, like he had expected. Last time he woke up, bandages were wrapped around his chest because—

"I found this letter," Yugi interrupted his thoughts. Yami blinked and looked down at the small note the younger one was holding in his hands. "You have to read it. It contains an important message."

Blinking, Yami took it from him and folded it open.

_Dear patients, _

_Due to technical difficulties, we had to reverse time and bring you back to the past. You are currently residing in the basement of the Domino Hospital and will be informed about our plans as soon as possible. Please don't panic for we have everything under control. We are working on a new system and experimenting with it so we will be able to get the best results. _

_Be patient and everything will fall into place._

_Yours sincerely, _

_Anonymous _

"Wait, who wrote this?" Yami said right after he had read it. The words had not even made sense to him. Nothing made sense to him anymore. Yugi shook his head and closed his eyes.

"They were not content with the operation, that is why they decided to turn back time and redo everything. The doors are locked, we can't get out. We've been here for a couple of hours already and there's no way they are going to let us out. All we can do is wait for them."

* * *

**Author's note: **I've been receiving several messages and reviews and since those were mostly anonymous messages, I couldn't reply and I know that most people don't read my profile, so... Translation (I wanted to make a theme-based message, but it was probably confusing): I was not happy with the outcome of the first chapter, I am rewriting it and will post it as soon as possible.

Please be patient, I know it's been two months, I'm extremely slow, y'all know that I'm a crappy updater. But the new first chapter will be here soon. :')


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